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- PDB-9ua8: structure of PTP-MEG2 and IFG1R-pY1165/pY1166 peptide complex -

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Basic information

Entry
Database: PDB / ID: 9ua8
Titlestructure of PTP-MEG2 and IFG1R-pY1165/pY1166 peptide complex
Components
  • THR-ASP-PTR-PTR-ARG
  • Tyrosine-protein phosphatase non-receptor type 9
KeywordsHYDROLASE / Complex.
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasm
Similarity search - Function
CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / : / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Protein tyrosine phosphatase, catalytic domain ...CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / : / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsHu, J. / Liu, H. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)T2422013 China
CitationJournal: J Exp Clin Cancer Res / Year: 2025
Title: PTPN9 dephosphorylates IGF1R Y1165/1166 and alleviates IGF1R-mediated resistance to tyrosine kinase inhibitor in cholangiocarcinoma.
Authors: Hu, J.M. / Liu, H.Q. / Zhang, M.H. / Chen, T.L. / Shi, A.D. / Gao, Q. / Liu, Y.J. / Wang, X. / Sun, K.Y. / Deng, J. / Xu, Y.F. / Pan, C. / Li, K.S. / Zhang, Z.L.
History
DepositionMar 31, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 9
F: THR-ASP-PTR-PTR-ARG
B: Tyrosine-protein phosphatase non-receptor type 9
C: THR-ASP-PTR-PTR-ARG
D: Tyrosine-protein phosphatase non-receptor type 9
E: THR-ASP-PTR-PTR-ARG
G: Tyrosine-protein phosphatase non-receptor type 9
H: THR-ASP-PTR-PTR-ARG


Theoretical massNumber of molelcules
Total (without water)144,4718
Polymers144,4718
Non-polymers00
Water3,963220
1
A: Tyrosine-protein phosphatase non-receptor type 9
F: THR-ASP-PTR-PTR-ARG


Theoretical massNumber of molelcules
Total (without water)36,1182
Polymers36,1182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-7 kcal/mol
Surface area12590 Å2
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 9
C: THR-ASP-PTR-PTR-ARG


Theoretical massNumber of molelcules
Total (without water)36,1182
Polymers36,1182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-8 kcal/mol
Surface area12550 Å2
MethodPISA
3
D: Tyrosine-protein phosphatase non-receptor type 9
E: THR-ASP-PTR-PTR-ARG


Theoretical massNumber of molelcules
Total (without water)36,1182
Polymers36,1182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-6 kcal/mol
Surface area12640 Å2
MethodPISA
4
G: Tyrosine-protein phosphatase non-receptor type 9
H: THR-ASP-PTR-PTR-ARG


Theoretical massNumber of molelcules
Total (without water)36,1182
Polymers36,1182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-8 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.294, 84.707, 52.675
Angle α, β, γ (deg.)86.03, 94.16, 90.05
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Tyrosine-protein phosphatase non-receptor type 9


Mass: 35110.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6IQ43, protein-tyrosine-phosphatase
#2: Protein/peptide
THR-ASP-PTR-PTR-ARG


Mass: 1006.886 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 318 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 4000, 0.2M KSCN, 10% ethelene glycol, 0.1M bis-tris propane

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.6→51 Å / Num. obs: 79491 / % possible obs: 95.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8
Reflection shellResolution: 1.6→1.68 Å / Rmerge(I) obs: 0.07 / Num. unique obs: 32748

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Processing

Software
NameVersionClassification
PHENIX1.6.2_432refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.999→36.77 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 25.81 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.254 3990 5.02 %
Rwork0.2167 --
obs0.2186 79491 91.91 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.938 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0071 Å20.425 Å20.5169 Å2
2---4.8708 Å22.3389 Å2
3---4.8637 Å2
Refinement stepCycle: LAST / Resolution: 1.999→36.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9541 0 0 220 9761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089836
X-RAY DIFFRACTIONf_angle_d1.17113335
X-RAY DIFFRACTIONf_dihedral_angle_d14.0813577
X-RAY DIFFRACTIONf_chiral_restr0.0721460
X-RAY DIFFRACTIONf_plane_restr0.0051702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.999-2.07040.33660.25147062X-RAY DIFFRACTION86
2.0704-2.15330.2963730.23637324X-RAY DIFFRACTION89
2.1533-2.25130.27093880.23377208X-RAY DIFFRACTION87
2.2513-2.36990.28383960.22937320X-RAY DIFFRACTION89
2.3699-2.51840.27633860.23387372X-RAY DIFFRACTION90
2.5184-2.71280.29233860.23427476X-RAY DIFFRACTION91
2.7128-2.98570.28514280.23617652X-RAY DIFFRACTION93
2.9857-3.41740.26034500.21217958X-RAY DIFFRACTION97
3.4174-4.30460.23134020.19888070X-RAY DIFFRACTION98
4.3046-9.5340.19964150.1958059X-RAY DIFFRACTION98

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